Symptoms
There are payments with the same number for the same provider, e.g. two payments with Document # 000588, but with the different ids.
Cause
The issue is caused by the bug with id #PBA-69470 ("Duplicate payment numbers"). Enumerator for payments has been reset to after reaching its limit.
Resolution
Change the enumerator for payments:
Home> System> Settings> More Finance Settings> Enumerator Classes > PAYMENT Payment Enum
for example it is set to 000590, change it by adding additional 0 to the beginning - 0000590 or 00000590.